>From git add --help

       -A, --all
           Like -u, but match <filepattern> against files in the working 
tree in addition to the index. That means that it will find new files as 
well as staging modified content and
           removing files that are no longer in the working tree.

In other words, "git add ." will only add new files and modified files to 
the index to be committed. It will not schedule removed files for deletion. 

If I've done a lot of restructuring, and moved a lot files around, I try to 
always use add -A so I don't forget committing file deletions.

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